cuPssmMaker.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistr.hpp>
#include <algo/blast/api/psiblast_options.hpp>
#include <algo/blast/api/pssm_engine.hpp>
#include <algo/structure/cd_utils/cuSequence.hpp>
#include <algo/structure/cd_utils/cuPssmMaker.hpp>
#include <algo/structure/cd_utils/cuPssmScorer.hpp>
#include <algo/structure/cd_utils/cuScoringMatrix.hpp>
#include <objects/scoremat/PssmFinalData.hpp>
#include <objects/scoremat/PssmIntermediateData.hpp>
#include <objects/cdd/Cdd_id.hpp>

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Functions
static void	printMsa (const char *filename, const PSIMsa *msa, vector< string > &seqIds)
int	findHighestScoringRowByPssm (CCdCore *ccd)

Function Documentation

findHighestScoringRowByPssm()

int findHighestScoringRowByPssm

(

CCdCore *

ccd

)

Definition at line 658 of file cuPssmMaker.cpp.

References bmp, CCdCore::GetBioseqForRow(), CCdCore::GetNumRows(), CCdCore::GetSeqAlign(), i, max(), and PssmScorer::score().

printMsa()

static void printMsa ( const char *  filename, const PSIMsa *  msa, vector< string > &  seqIds  )

static

Definition at line 51 of file cuPssmMaker.cpp.

References ASSERT, PSIMsa::data, PSIMsa::dimensions, fp, ColumnResidueProfile::getEaaCode(), i, PSIMsaCell::is_aligned, PSIMsaCell::letter, NULL, PSIMsaDimensions::num_seqs, and PSIMsaDimensions::query_length.

Referenced by PssmMaker::printAlignment().